Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1321 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1218193308 sf1218164744 12 18193308 1.31E-09 1.31E-09
vg0322732625 sf0322731114 3 22732625 9.74E-07 9.74E-07
vg0906198689 sf0906197689 9 6198689 1.49E-06 1.49E-06
vg0521727029 sf0521664471 5 21727029 1.63E-06 1.63E-06
vg0312535741 sf0312534459 3 12535741 1.65E-06 1.65E-06
vg1216729892 sf1216723846 12 16729892 2.99E-06 2.99E-06
vg0216380020 sf0216374150 2 16380020 3.06E-06 3.06E-06
vg0707304200 sf0707303205 7 7304200 4.06E-06 4.06E-06
vg1217854218 sf1217825652 12 17854218 4.10E-06 4.10E-06